Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0004163

Physical Location & Seq

Genomic Coordinates Forward (+)

15299701 .. 15304866

Gene Structure 5166 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG150800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1005 bp

ATGGCAACGGCTTTCTCTTTTGCCCAAACTGTTCTCTTCTCCAAAACCTCACTCTCTCTCCGCACCAATGCCCTCAGAAGCTTAACCTTCTGCCTACCTTTCTCTTCTTCTTCTGCAGCTCTTGCCTCTGATAAGCCTCACAGCAAAAAATGGAGGCAGCCAGTGACTTCGGCGCTGGAGCTCGGCGGCGTCAAGATTGCTAAAGATGATGTGTTGAGGGATGACCCCACAAACAATGTTCCGGATACAATTTTTGCAAAGCTTGGAATGCAACTGCATAGAAGAGATCAGCACCCACTTGGAATTCTGAAGAATGCTATATATGAATACTTTGACACCAATTACTCAAACAAGTTTGATAAGTTCGATGATCTTTGCCCACTTGTATCTGTTAAGGAGAATTTTGATGATGTATTAGTTCCTGCTGATCACGTGAGTCGAAGTTATAATGATACATACTATGTGGACTCTCAAACAGTTTTGAGGTGCCATACAAGTGCTCATCAGGCAGAGTTATTGAGAAGAGGACATACTCATTTCCTTGTAACTGGAGATGTGTACCGTAGGGATTCCATCGACTCTACACATTACCCTGTGTTCCATCAGATGGAAGGGGTTCGTGTTTTTTCTCCAGAAGATTGGGCAGCATCTGGGGCAGATGCAACATCTTATGTAGCTGAGGACTTGAAGAAATGCCTTGAGGGCTTGGCACGCCACCTATTTGGTGCTGTGGAGATGCGCTGGGTTGATACATACTTTCCATTTACCAATCCATCATTTGAACTTGAGATTTTCTTTCAGGAAAAGTGGTTGGAGGTTTTGGGTTGCGGAGTAACAGAACAAGAAATATTGAAGAGAAGTGGCAAAACAAACAATGTTGCTTGGGCTTTCGGACTTGGATTGGAGCGGCTGGCAATGGTTCTATTTGAAATCCCTGATATTCGCCTTTTCTGGTCAACTGATGAGAGGTTTACCTCGCAGGTGGTTCCTGTACCCATTAAATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0004812 GO:0004826 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0006082 GO:0006139 GO:0006399 GO:0006412 GO:0006418 GO:0006432 GO:0006518 GO:0006520 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009507 GO:0009532 GO:0009536 GO:0009570 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016874 GO:0016875 GO:0019538 GO:0019752 GO:0034641 GO:0034645 GO:0034660 GO:0043038 GO:0043039 GO:0043043 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043436 GO:0043603 GO:0043604 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044281 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:0140098 GO:0140101 GO:1901360 GO:1901564 GO:1901566 GO:1901576

KEGG Pathways

Metabolic & Signaling

ko00970 map00970

Pfam Domains

Protein Families

FDX-ACB tRNA-synt_2d

Protein Analysis

334

Amino Acids

37.97

Weight (kDa)

5.89

Isoelectric Point (pI)

40.51

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
tRNA-synt_2d	PF01409	97 - 327	7.8e-49	tRNA synthetases class II core domain (F)

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Orthologous Genes (Group: OG0004163)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G58140
fragaria_vesca	FvH4_3g12680 FvH4_3g12680 FvH4_3g12680
malus_domestica	MD05G1248600.v1.1 MD10G1229100.v1.1
prunus_persica	Prupe.4G115500_v2.0.a1
pyrus_communis	pycom05g22530 pycom10g19270
rosa_chinensis	RchiOBHm_Chr3g0486261 RchiOBHm_Chr5g0020641
rosa_laevigata	RLG00000023089 RLG00000032549
rosa_multiflora	Rmu_sc0001857.1_g000018 Rmu_sc0005607.1_g000020 Rmu_sc0005842.1_g000003 Rmu_sc0007661.1_g000010
rosa_roxburghii	Rroxscaffold_1G00057630 Rroxscaffold_6G00395930
rosa_rugosa	Rorug03G0224300 Rorug03G0224400 Rorug03G0224500 Rorug05G0062200
rosa_samantha	Rh3AG274300 Rh3BG309600 Rh3CG308800 Rh5AG151900 Rh5BG151600 Rh5CG162900 Rh5DG150800
rosa_wichuraiana	Rw0G022550 Rw3G024320 Rw5G013460

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	447
AarI	CACCTGC	1 cut(s)	970
Acc36I	ACCTGC	1 cut(s)	970
AccB1I	GGYRCC	1 cut(s)	486
AccB7I	CCANNNNNTGG	1 cut(s)	607
AccBSI	CCGCTC	1 cut(s)	907
AccIII	TCCGGA	1 cut(s)	241
AciI	CCGC	4 cut(s)	61, 186, 828, 907
AcsI	RAATTY	2 cut(s)	303, 400
AcuI	CTGAAG	1 cut(s)	329
AcvI	CACGTG	1 cut(s)	433
AcyI	GRCGYC	1 cut(s)	189
AfaI	GTAC	2 cut(s)	560, 993
AfiI	CCNNNNNNNGG	1 cut(s)	607
AgsI	TTSAA	4 cut(s)	688, 782, 853, 929
AluBI	AGCT	5 cut(s)	81, 119, 181, 262, 677
AluI	AGCT	5 cut(s)	81, 119, 181, 262, 677
Alw21I	GWGCWC	2 cut(s)	183, 502
AlwNI	CAGNNNCTG	1 cut(s)	650
Aor13HI	TCCGGA	1 cut(s)	241
ApeKI	GCWGC	3 cut(s)	116, 157, 644
ApoI	RAATTY	2 cut(s)	303, 400
Asp700I	GAANNNNTTC	1 cut(s)	615
AspLEI	GCGC	2 cut(s)	175, 741
BanI	GGYRCC	1 cut(s)	486
BanII	GRGCYC	1 cut(s)	183
BarI	GAAGNNNNNNTAC	2 cut(s)	514, 546
BbrPI	CACGTG	1 cut(s)	433
Bbv12I	GWGCWC	2 cut(s)	183, 502
BbvCI	CCTCAGC	1 cut(s)	678
BbvI	GCAGC	3 cut(s)	128, 169, 656
BccI	CCATC	4 cut(s)	581, 601, 609, 781
BceAI	ACGGC	1 cut(s)	24
BciVI	GTATCC	1 cut(s)	238
BclI	TGATCA	1 cut(s)	427
BfmI	CTRYAG	1 cut(s)	114
BfoI	RGCGCY	1 cut(s)	176
BfuAI	ACCTGC	1 cut(s)	970
BfuI	GTATCC	1 cut(s)	238
BglI	GCCNNNNNGGC	1 cut(s)	702
BisI	GCNGC	5 cut(s)	117, 158, 187, 645, 908
BlsI	GCNGC	5 cut(s)	118, 159, 188, 646, 909
BmiI	GGNNCC	2 cut(s)	488, 987
BmsI	GCATC	3 cut(s)	649, 656, 726
BpmI	CTGGAG	3 cut(s)	197, 570, 615
Bpu10I	CCTNAGC	1 cut(s)	678
BpuEI	CTTGAG	2 cut(s)	719, 806
BsaAI	YACGTR	1 cut(s)	433
BsaHI	GRCGYC	1 cut(s)	189
BsaWI	WCCGGW	1 cut(s)	241
BsaXI	ACNNNNNCTCC	2 cut(s)	42, 72
Bsc4I	CCNNNNNNNGG	1 cut(s)	607
Bse1I	ACTGG	2 cut(s)	161, 553
Bse3DI	GCAATG	1 cut(s)	921
BseAI	TCCGGA	1 cut(s)	241
BseGI	GGATG	1 cut(s)	226
BseLI	CCNNNNNNNGG	1 cut(s)	607
BseMI	GCAATG	1 cut(s)	921
BseMII	CTCAG	2 cut(s)	88, 669
BseNI	ACTGG	2 cut(s)	161, 553
BseXI	GCAGC	3 cut(s)	128, 169, 656
BseYI	CCCAGC	1 cut(s)	741
BshNI	GGYRCC	1 cut(s)	486
BsiHKAI	GWGCWC	2 cut(s)	183, 502
BsiSI	CCGG	1 cut(s)	242
BslI	CCNNNNNNNGG	1 cut(s)	607
BsmI	GAATGC	2 cut(s)	273, 319
Bsp1286I	GDGCHC	2 cut(s)	183, 502
Bsp13I	TCCGGA	1 cut(s)	241
Bsp143I	GATC	3 cut(s)	286, 370, 427
BspACI	CCGC	4 cut(s)	61, 186, 828, 907
BspCNI	CTCAG	2 cut(s)	87, 670
BspEI	TCCGGA	1 cut(s)	241
BspLI	GGNNCC	2 cut(s)	488, 987
BspMAI	CTGCAG	1 cut(s)	118
BspMI	ACCTGC	1 cut(s)	970
BspT107I	GGYRCC	1 cut(s)	486
BsrBI	CCGCTC	1 cut(s)	907
BsrDI	GCAATG	1 cut(s)	921
BsrI	ACTGG	2 cut(s)	161, 553
BssMI	GATC	3 cut(s)	286, 370, 427
BssNI	GRCGYC	1 cut(s)	189
Bst4CI	ACNGT	3 cut(s)	31, 478, 563
Bst6I	CTCTTC	5 cut(s)	41, 109, 277, 517, 848
BstACI	GRCGYC	1 cut(s)	189
BstAPI	GCANNNNNTGC	1 cut(s)	122
BstBAI	YACGTR	1 cut(s)	433
BstC8I	GCNNGC	2 cut(s)	712, 912
BstDEI	CTNAG	2 cut(s)	74, 678
BstF5I	GGATG	1 cut(s)	226
BstH2I	RGCGCY	1 cut(s)	176
BstHHI	GCGC	2 cut(s)	175, 741
BstKTI	GATC	3 cut(s)	289, 373, 430
BstMBI	GATC	3 cut(s)	286, 370, 427
BstMWI	GCNNNNNNNGC	6 cut(s)	122, 268, 506, 653, 702, 711
BstSFI	CTRYAG	1 cut(s)	114
BstV1I	GCAGC	3 cut(s)	128, 169, 656
BstXI	CCANNNNNNTGG	2 cut(s)	639, 722
BsuI	GTATCC	1 cut(s)	238
BtsCI	GGATG	1 cut(s)	226
BtsIMutI	CAGTG	1 cut(s)	168
BveI	ACCTGC	1 cut(s)	970
Cac8I	GCNNGC	2 cut(s)	712, 912
CaiI	CAGNNNCTG	1 cut(s)	650
CfoI	GCGC	2 cut(s)	175, 741
CseI	GACGC	1 cut(s)	178
Csp6I	GTAC	2 cut(s)	559, 992
CviQI	GTAC	2 cut(s)	559, 992
DdeI	CTNAG	2 cut(s)	74, 678
DpnI	GATC	3 cut(s)	288, 372, 429
DpnII	GATC	3 cut(s)	286, 370, 427
Eam1104I	CTCTTC	5 cut(s)	41, 109, 277, 517, 848
EarI	CTCTTC	5 cut(s)	41, 109, 277, 517, 848
Ecl136II	GAGCTC	1 cut(s)	181
Eco24I	GRGCYC	1 cut(s)	183
Eco53kI	GAGCTC	1 cut(s)	181
Eco57I	CTGAAG	1 cut(s)	329
Eco72I	CACGTG	1 cut(s)	433
EcoICRI	GAGCTC	1 cut(s)	181
EcoRI	GAATTC	1 cut(s)	303
EcoT38I	GRGCYC	1 cut(s)	183
FbaI	TGATCA	1 cut(s)	427
Fnu4HI	GCNGC	5 cut(s)	117, 158, 187, 645, 908
FokI	GGATG	1 cut(s)	233
FriOI	GRGCYC	1 cut(s)	183
Fsp4HI	GCNGC	5 cut(s)	117, 158, 187, 645, 908
GlaI	GCGC	2 cut(s)	174, 740
GluI	GCNGC	5 cut(s)	117, 158, 187, 645, 908
GsaI	CCCAGC	1 cut(s)	745
GsuI	CTGGAG	3 cut(s)	197, 570, 615
HaeII	RGCGCY	1 cut(s)	176
HapII	CCGG	1 cut(s)	242
HgaI	GACGC	1 cut(s)	178
HhaI	GCGC	2 cut(s)	175, 741
Hin1I	GRCGYC	1 cut(s)	189
Hin6I	GCGC	2 cut(s)	173, 739
HinP1I	GCGC	2 cut(s)	173, 739
HincII	GTYRAC	1 cut(s)	957
HindII	GTYRAC	1 cut(s)	957
HindIII	AAGCTT	2 cut(s)	79, 260
HinfI	GANTC	4 cut(s)	436, 467, 569, 578
HpaII	CCGG	1 cut(s)	242
Hpy166II	GTNNAC	4 cut(s)	466, 559, 957, 972
Hpy188I	TCNGA	5 cut(s)	77, 130, 309, 606, 893
Hpy188III	TCNNGA	4 cut(s)	193, 242, 632, 800
Hpy8I	GTNNAC	4 cut(s)	466, 559, 957, 972
HpyAV	CCTTC	2 cut(s)	97, 605
HpyCH4III	ACNGT	3 cut(s)	31, 478, 563
HpyCH4IV	ACGT	1 cut(s)	432
HpyCH4V	TGCA	5 cut(s)	116, 257, 271, 277, 662
HpyF10VI	GCNNNNNNNGC	6 cut(s)	122, 268, 506, 653, 702, 711
HpyF3I	CTNAG	2 cut(s)	74, 678
HpySE526I	ACGT	1 cut(s)	432
Hsp92I	GRCGYC	1 cut(s)	189
HspAI	GCGC	2 cut(s)	173, 739
Kpn2I	TCCGGA	1 cut(s)	241
Ksp22I	TGATCA	1 cut(s)	427
Kzo9I	GATC	3 cut(s)	286, 370, 427
LmnI	GCTCC	2 cut(s)	178, 904
Lsp1109I	GCAGC	3 cut(s)	128, 169, 656
LweI	GCATC	3 cut(s)	649, 656, 726
MaeII	ACGT	1 cut(s)	432
MaeIII	GTNAC	3 cut(s)	163, 544, 832
MalI	GATC	3 cut(s)	288, 372, 429
MbiI	CCGCTC	1 cut(s)	907
MboI	GATC	3 cut(s)	286, 370, 427
MhlI	GDGCHC	2 cut(s)	183, 502
MluCI	AATT	4 cut(s)	249, 303, 340, 400
MlyI	GAGTC	3 cut(s)	445, 461, 572
MmeI	TCCRAC	1 cut(s)	792
MroI	TCCGGA	1 cut(s)	241
MroXI	GAANNNNTTC	1 cut(s)	615
MseI	TTAA	3 cut(s)	83, 393, 999
MslI	CAYNNNNRTG	1 cut(s)	495
MspI	CCGG	1 cut(s)	242
Mva1269I	GAATGC	2 cut(s)	273, 319
MwoI	GCNNNNNNNGC	6 cut(s)	122, 268, 506, 653, 702, 711
NdeII	GATC	3 cut(s)	286, 370, 427
NlaIV	GGNNCC	2 cut(s)	488, 987
NmeAIII	GCCGAG	1 cut(s)	162
NmuCI	GTSAC	1 cut(s)	163
PaqCI	CACCTGC	1 cut(s)	970
PctI	GAATGC	2 cut(s)	273, 319
PdmI	GAANNNNTTC	1 cut(s)	615
PfeI	GAWTC	1 cut(s)	569
PflMI	CCANNNNNTGG	1 cut(s)	607
PkrI	GCNGC	5 cut(s)	118, 159, 188, 646, 909
PleI	GAGTC	3 cut(s)	444, 461, 572
PmaCI	CACGTG	1 cut(s)	433
PmlI	CACGTG	1 cut(s)	433
PpsI	GAGTC	3 cut(s)	444, 461, 572
Ppu21I	YACGTR	1 cut(s)	433
PsiI	TTATAA	1 cut(s)	447
Psp124BI	GAGCTC	1 cut(s)	183
PspCI	CACGTG	1 cut(s)	433
PspFI	CCCAGC	1 cut(s)	741
PspN4I	GGNNCC	2 cut(s)	488, 987
PstI	CTGCAG	1 cut(s)	118
PstNI	CAGNNNCTG	1 cut(s)	650
RsaI	GTAC	2 cut(s)	560, 993
RsaNI	GTAC	2 cut(s)	559, 992
RseI	CAYNNNNRTG	1 cut(s)	495
SacI	GAGCTC	1 cut(s)	183
SaqAI	TTAA	3 cut(s)	83, 393, 999
SatI	GCNGC	5 cut(s)	117, 158, 187, 645, 908
Sau3AI	GATC	3 cut(s)	286, 370, 427
SchI	GAGTC	3 cut(s)	445, 461, 572
SduI	GDGCHC	2 cut(s)	183, 502
SfaNI	GCATC	3 cut(s)	649, 656, 726
SfcI	CTRYAG	1 cut(s)	114
SmiMI	CAYNNNNRTG	1 cut(s)	495
SmlI	CTYRAG	2 cut(s)	698, 785
SmoI	CTYRAG	2 cut(s)	698, 785
Sse9I	AATT	4 cut(s)	249, 303, 340, 400
SsiI	CCGC	4 cut(s)	61, 186, 828, 907
SspI	AATATT	1 cut(s)	849
SstI	GAGCTC	1 cut(s)	183
TaaI	ACNGT	3 cut(s)	31, 478, 563
TaiI	ACGT	1 cut(s)	435
TaqI	TCGA	3 cut(s)	366, 439, 576
TasI	AATT	4 cut(s)	249, 303, 340, 400
TauI	GCSGC	2 cut(s)	189, 910
TfiI	GAWTC	1 cut(s)	569
Tru1I	TTAA	3 cut(s)	83, 393, 999
Tru9I	TTAA	3 cut(s)	83, 393, 999
TscAI	CASTG	1 cut(s)	168
TseFI	GTSAC	1 cut(s)	163
TseI	GCWGC	3 cut(s)	116, 157, 644
Tsp45I	GTSAC	1 cut(s)	163
TspDTI	ATGAA	1 cut(s)	339
TspRI	CASTG	1 cut(s)	168
Van91I	CCANNNNNTGG	1 cut(s)	607
XapI	RAATTY	2 cut(s)	303, 400
XmnI	GAANNNNTTC	1 cut(s)	615

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.